Use "ubuntu-slim" for most workflows by koppor · Pull Request #15019 · JabRef/jabref

koppor · 2026-02-03T18:05:51Z

User description

Today, I learned that there is "ubuntu-slim". We don't need the large runners for worklows such as issue-unassigment.

I tried at most jobs to use slim. Let's see, how it goes. We can use the normal ones as soon as they fail.

Source: https://docs.github.com/en/actions/reference/runners/github-hosted-runners

Also applies gradle-update/update-gradle-wrapper-action#988 (comment) to have the gradle update working again.

Steps to test

See CI jobs running with 5 GB RAM (instead of 16 GB)

Mandatory checks

I own the copyright of the code submitted and I license it under the MIT license
[/] I manually tested my changes in running JabRef (always required)
[/] I added JUnit tests for changes (if applicable)
[/] I added screenshots in the PR description (if change is visible to the user)
[/] I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
[/] I checked the user documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

PR Type

Enhancement

Description

Replace ubuntu-latest with ubuntu-slim across all GitHub Actions workflows
Reduces resource consumption from 16 GB to 5 GB RAM for CI jobs
Applies change to 40+ workflow files for consistency
Removes unused product-map.yml workflow file

Diagram Walkthrough

flowchart LR
  A["GitHub Actions Workflows"] -->|"Replace runner"| B["ubuntu-latest"]
  B -->|"Change to"| C["ubuntu-slim"]
  C -->|"Result"| D["5 GB RAM instead of 16 GB"]
  D -->|"Benefit"| E["Reduced resource usage"]

File Walkthrough

Relevant files

Configuration changes

34 files

automerge.yml `Update runner to ubuntu-slim`	+1/-1
binaries.yml `Update multiple jobs to ubuntu-slim`	+4/-4
check-links.yml `Update runner to ubuntu-slim`	+1/-1
cleanup-pr.yml `Update runner to ubuntu-slim`	+1/-1
delete-old-runs-manually.yml `Update runner to ubuntu-slim`	+1/-1
issue-comment.yml `Update runner to ubuntu-slim`	+1/-1
latex.yml `Update multiple jobs to ubuntu-slim`	+2/-2
link-issue.yml `Update multiple jobs to ubuntu-slim`	+3/-3
on-issue-comment.yml `Update runner to ubuntu-slim`	+1/-1
on-issue-labeled.yml `Update multiple jobs to ubuntu-slim`	+6/-6
on-issue-unassigned.yml `Update runner to ubuntu-slim`	+1/-1
on-issue-unlabeled.yml `Update runner to ubuntu-slim`	+1/-1
on-pr-changes-requested-check.yml `Update runner to ubuntu-slim`	+1/-1
on-pr-changes-requested-move-labels.yml `Update runner to ubuntu-slim`	+1/-1
on-pr-closed.yml `Update multiple jobs to ubuntu-slim`	+5/-5
on-pr-labeled-update-pr-status.yml `Update runner to ubuntu-slim`	+1/-1
on-pr-labeled.yml `Update multiple jobs to ubuntu-slim`	+2/-2
on-pr-merge-queued.yml `Update runner to ubuntu-slim`	+1/-1
on-pr-opened-updated-check.yml `Update runner to ubuntu-slim`	+1/-1
on-pr-opened.yml `Update runner to ubuntu-slim`	+1/-1
pages.yml `Update multiple jobs to ubuntu-slim`	+2/-2
pr-changelog.yml `Update multiple jobs to ubuntu-slim`	+2/-2
pr-comment.yml `Update runner to ubuntu-slim`	+1/-1
pr-format.yml `Update multiple jobs to ubuntu-slim`	+4/-4
pr-modifications.yml `Update multiple jobs to ubuntu-slim`	+5/-5
publish.yml `Update runner to ubuntu-slim`	+1/-1
rerun-merge-conflict-check.yml `Update runner to ubuntu-slim`	+1/-1
sbom-pr.yml `Update runner to ubuntu-slim`	+1/-1
stale.yml `Update runner to ubuntu-slim`	+1/-1
tests-code-fetchers.yml `Update runner to ubuntu-slim`	+1/-1
tests-code.yml `Update multiple jobs to ubuntu-slim`	+18/-18
unassign-issues.yml `Update multiple jobs to ubuntu-slim`	+2/-2
update-gradle-wrapper.yml `Update runner to ubuntu-slim`	+1/-1
upload-release.yml `Update runner to ubuntu-slim`	+1/-1

Miscellaneous

1 files

product-map.yml `Remove unused workflow file`	+0/-32

qodo-free-for-open-source-projects · 2026-02-03T18:06:31Z

PR Compliance Guide 🔍

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	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
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qodo-free-for-open-source-projects · 2026-02-03T18:07:48Z

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	✅ ~~Revert to ubuntu-latest for TeX Live~~ Suggestion Impact: The commit changed the check-latex job's runner from ubuntu-slim to ubuntu-latest and added a comment explaining why texlive doesn't run on ubuntu-slim. This directly addresses the suggestion's concern about the install-texlive action's dependencies. code diff: - runs-on: ubuntu-slim + # texlive doesn't run on ubuntu-slim + runs-on: ubuntu-latest Revert the runner from `ubuntu-slim` to `ubuntu-latest` for the `cache` and `check-latex` jobs. The `install-texlive` action they use has dependencies not available in the slim image, which would cause the workflow to fail. .github/workflows/latex.yml [24-44] jobs: cache: if: ${{ github.repository_owner == 'JabRef' }} - runs-on: ubuntu-slim + runs-on: ubuntu-latest steps: - name: Check out code uses: actions/checkout@v6 - name: Install TeX Live uses: zauguin/install-texlive@v4 with: package_file: jablib/src/test/latex/Texlivefile check-latex: needs: [ cache ] - runs-on: ubuntu-slim + runs-on: ubuntu-latest strategy: fail-fast: false matrix: include: - os: ubuntu-latest module: jabref testtask: checkLatex ... `[To ensure code accuracy, apply this suggestion manually]` Suggestion importance[1-10]: 9 __ Why: The suggestion correctly identifies that the `zauguin/install-texlive@v4` action requires dependencies like `perl` which are not present in the `ubuntu-slim` image, preventing a likely CI failure.	High
	✅ ~~Install jq dependency for ubuntu-slim~~ Suggestion Impact: The suggestion identified the need to install jq on ubuntu-slim runners. The commit implemented this requirement but used a different approach - instead of direct apt-get commands, it used the awalsh128/cache-apt-pkgs-action GitHub Action to install jq with caching capabilities. The same three jobs were modified as suggested. code diff: + - uses: awalsh128/cache-apt-pkgs-action@latest + with: + packages: jq + version: 1.0 - name: "good first issue" env: GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }} @@ -98,6 +102,10 @@ if: github.event.label.name == 'needs-refinement' && github.repository_owner == 'JabRef' runs-on: ubuntu-slim steps: + - uses: awalsh128/cache-apt-pkgs-action@latest + with: + packages: jq + version: 1.0 - name: needs-refinement env: GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }} @@ -109,6 +117,10 @@ if: "${{ github.event.label.name == 'status: freeze' && github.repository_owner == 'JabRef' }}" runs-on: ubuntu-slim steps: + - uses: awalsh128/cache-apt-pkgs-action@latest + with: + packages: jq + version: 1.0 Install `jq` in the `good-first-issue`, `needs-refinement`, and `status-freeze` jobs. The `ubuntu-slim` runner does not include `jq` by default, which is necessary for these jobs to run. .github/workflows/on-issue-labeled.yml [86-117] ... good-first-issue: name: "good first issue" if: "${{ github.event.label.name == 'good first issue' && github.repository_owner == 'JabRef' }}" runs-on: ubuntu-slim steps: + - name: Install jq + run: sudo apt-get update && sudo apt-get install -y jq - name: "good first issue" env: GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }} run: \| ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH") gh project item-add 5 --owner JabRef --url $ISSUE_URL needs-refinement: if: github.event.label.name == 'needs-refinement' && github.repository_owner == 'JabRef' runs-on: ubuntu-slim steps: + - name: Install jq + run: sudo apt-get update && sudo apt-get install -y jq - name: needs-refinement env: GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }} run: \| ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH") gh project item-add 15 --owner JabRef --url $ISSUE_URL status-freeze: name: "status: freeze" if: "${{ github.event.label.name == 'status: freeze' && github.repository_owner == 'JabRef' }}" runs-on: ubuntu-slim steps: + - name: Install jq + run: sudo apt-get update && sudo apt-get install -y jq - name: "status: freeze" env: GH_TOKEN: ${{ secrets.GH_TOKEN_PROJECT_ITEM_ADD }} run: \| ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH") gh project item-add 9 --owner JabRef --url $ISSUE_URL ... `[To ensure code accuracy, apply this suggestion manually]` Suggestion importance[1-10]: 8 __ Why: The suggestion correctly points out that `jq` is missing in `ubuntu-slim` and is required by multiple jobs in the workflow, thus preventing a CI failure.	Medium
	✅ ~~Install wget dependency for ubuntu-slim~~ Suggestion Impact: The suggestion identified the issue that ubuntu-slim lacks wget. Instead of installing wget as suggested, the commit solved the problem by switching from ubuntu-slim to ubuntu-latest, which includes wget by default. The comment in the commit explicitly references the wget issue mentioned in the suggestion. code diff: - runs-on: ubuntu-slim + # ubuntu-slim does not contain wget (and we don't have time for apt-get install wget during the release phase) + runs-on: ubuntu-latest Install `wget` in the `release` job. The `ubuntu-slim` runner does not include `wget` by default, which is needed to download binaries. .github/workflows/upload-release.yml [11-24] jobs: release: runs-on: ubuntu-slim steps: + - name: Install wget + run: sudo apt-get update && sudo apt-get install -y wget - name: Get binaries from builds.jabref.org run: \| mkdir build cd build wget -q -m -r -nH --cut-dirs 2 --no-parent --accept=tar.gz,dmg,pkg,deb,rpm,zip,msi https://builds.jabref.org/tags/ - name: Release uses: softprops/action-gh-release@v2 with: draft: true files: build/** `[Suggestion processed]` Suggestion importance[1-10]: 8 __ Why: The suggestion correctly identifies that `wget` is not available on `ubuntu-slim` and is required by the `release` job, preventing a workflow failure.	Medium
High-level	✅ ~~Consider a phased rollout for runner migration~~ Suggestion Impact: The commit demonstrates a rollback/correction approach that aligns with the suggestion's risk mitigation philosophy. Instead of keeping all workflows on ubuntu-slim, the commit reverts specific workflows back to ubuntu-latest where ubuntu-slim proved problematic (format job needs docker, maven-examples needs specific capabilities). This shows validation and adjustment based on testing, which is the core intent of the phased rollout suggestion - identifying and fixing issues incrementally rather than facing widespread failures. code diff: format: - runs-on: ubuntu-slim + # ubuntu-slim doesn't offer docker + runs-on: ubuntu-latest steps: - uses: actions/checkout@v6 - uses: leventeBajczi/intellij-idea-format@master @@ -445,8 +446,8 @@ shell: bash maven-examples: - name: Maven examples (main) - runs-on: ubuntu-slim + name: Maven examples + runs-on: ubuntu-latest needs: publish if: github.ref == 'refs/heads/main' strategy: @@ -471,33 +472,6 @@ mvn --batch-mode --update-snapshots verify shell: bash - maven-pr: - name: Maven examples (PR) - runs-on: ubuntu-slim - # does not need publish, because there is no publishing on non-main - if: github.ref != 'refs/heads/main' - strategy: - fail-fast: false - matrix: - project: [ jablib-examples/maven3/doi-to-bibtex ] - steps: - - name: Checkout source - uses: actions/checkout@v6 - with: - submodules: 'false' - show-progress: 'false' - - name: Set up JDK - uses: actions/setup-java@v5 - with: - java-version: 24 - distribution: 'corretto' - cache: maven - check-latest: true - - run: \| - cd ${{ matrix.project }} - mvn --batch-mode --update-snapshots verify - shell: bash To mitigate the risk of widespread CI failures, this suggestion recommends migrating workflows from `ubuntu-latest` to `ubuntu-slim` in smaller, incremental batches rather than all at once. This allows for validating changes on simpler workflows before applying them to more complex ones. Examples: .github/workflows/automerge.yml [10] runs-on: ubuntu-slim .github/workflows/tests-code.yml [34-576] runs-on: ubuntu-slim steps: - name: Create pr_number.txt run: echo "${{ github.event.number }}" > pr_number.txt - uses: actions/upload-artifact@v6 with: name: pr_number path: pr_number.txt checkstyle: ... (clipped 533 lines) Solution Walkthrough: Before: # In a single PR, all workflows are changed simultaneously. # .github/workflows/automerge.yml jobs: automerge: runs-on: ubuntu-slim # was ubuntu-latest # .github/workflows/binaries.yml jobs: conditions: runs-on: ubuntu-slim # was ubuntu-latest build: runs-on: ubuntu-latest # This one was missed in the PR ... # ... and so on for over 40 workflow files. After: # Suggested approach: A series of smaller PRs. # PR 1: Migrate simple, low-risk workflows. # .github/workflows/automerge.yml jobs: automerge: runs-on: ubuntu-slim # was ubuntu-latest # PR 2 (after PR 1 is validated): Migrate more complex workflows. # .github/workflows/binaries.yml jobs: conditions: runs-on: ubuntu-slim # was ubuntu-latest ... Suggestion importance[1-10]: 8 __ Why: This suggestion addresses a significant risk of widespread CI failure by proposing a safer, phased rollout strategy, which is a crucial consideration for a large-scale infrastructure change.	Medium
Update

qodo-free-for-open-source-projects · 2026-02-03T20:29:08Z

CI Feedback 🧐

A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

Action: Fetcher tests
Failed stage: Run fetcher tests [❌]
Failed test name: Multiple tests failed, primarily in ArXivFetcherTest, ISIDOREFetcherTest, LibraryOfCongressTest, ZbMATHTest, GrobidPlainCitationParserTest, and URLDownloadTest
Failure summary: The action failed because multiple test suites in the `fetcherTest` task encountered failures. The main categories of failures include: - ArXiv URL scheme mismatches: Many `ArXivFetcherTest` tests failed because they expected URLs with `http://` scheme but received `https://` scheme instead (e.g., `expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]>` at line 1175-1176). - Network connectivity issues: Several tests failed due to network problems: - SSL certificate validation failures in `ISIDOREFetcherTest` (lines 2206-2211, 2216-2221, 2226-2231) - Connection timeouts in `LibraryOfCongressTest` (lines 2237-2238, 2245-2246) - HTTP 403 errors from zbMATH API (lines 2313-2314, 2320-2321) - HTTP 429 (Too Many Requests) errors from GitHub (lines 2564-2565) - Grobid service connection failures with `UnresolvedAddressException` (lines 2481-2486, 2491-2496, etc.) - API response changes: Tests failed due to unexpected API responses: - Semantic Scholar API returned 404 errors (lines 2303-2305) - Empty search results where entries were expected (line 1282-1283) - Missing or changed metadata fields in fetched entries - Test data mismatches: Several tests failed due to differences in expected vs actual bibliographic entry data, including missing authors, changed field values, or different metadata structures. The build failed with 58 out of 508 tests failing, primarily in the `:jablib:fetcherTest` task.
Relevant error logs: 1: ##[group]Runner Image Provisioner 2: Hosted Compute Agent ... 434: 32M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-darwin-amd64/18.1.0 435: 32M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-darwin-amd64 436: 15M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-linux-amd64-alpine/18.1.0/cc208b257571554934ff0e57a5e3e3029ebfeaac 437: 15M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-linux-amd64-alpine/18.1.0 438: 15M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-linux-amd64-alpine 439: 15M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-linux-amd64/18.1.0/3e631dd2a732608362a6900aa81fa3a16aaf4977 440: 15M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-linux-amd64/18.1.0 441: 15M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-linux-amd64 442: 25M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-windows-amd64/18.1.0/4033aaf4977affcf6c25b6ffa017630709dd6411 443: 25M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-windows-amd64/18.1.0 444: 25M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-windows-amd64 445: 32M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-darwin-arm64v8/18.1.0/5941b043f17fe3deca920763efd2fc38ed2f0efa 446: 32M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-darwin-arm64v8/18.1.0 447: 32M ./caches/modules-2/files-2.1/io.zonky.test.postgres/embedded-postgres-binaries-darwin-arm64v8 448: 130M ./caches/modules-2/files-2.1/io.zonky.test.postgres 449: 5.1M ./caches/modules-2/files-2.1/io.github.eisop/dataflow-errorprone/3.41.0-eisop1/3fc86eff95c549e42c41fd7c01c2a57ed46a5a94 450: 5.1M ./caches/modules-2/files-2.1/io.github.eisop/dataflow-errorprone/3.41.0-eisop1 451: 5.1M ./caches/modules-2/files-2.1/io.github.eisop/dataflow-errorprone 452: 5.1M ./caches/modules-2/files-2.1/io.github.eisop ... 649: JAVA_HOME_25_X64: /opt/hostedtoolcache/Java_Corretto_jdk/25.0.2-10.1/x64 650: GRADLE_ACTION_ID: gradle/actions/setup-gradle 651: GRADLE_USER_HOME: /home/runner/.gradle 652: GRADLE_BUILD_ACTION_SETUP_COMPLETED: true 653: GRADLE_BUILD_ACTION_CACHE_RESTORED: true 654: DEVELOCITY_INJECTION_INIT_SCRIPT_NAME: gradle-actions.inject-develocity.init.gradle 655: DEVELOCITY_INJECTION_CUSTOM_VALUE: gradle-actions 656: GITHUB_DEPENDENCY_GRAPH_ENABLED: false 657: CI: true 658: ##[endgroup] 659: Starting a Gradle Daemon (subsequent builds will be faster) 660: Parallel Configuration Cache is an incubating feature. 661: Configuration on demand is an incubating feature. 662: Calculating task graph as no cached configuration is available for tasks: fetcherTest 663: Kotlin does not yet support 25 JDK target, falling back to Kotlin JVM_24 JVM target 664: > Task :build-logic:checkKotlinGradlePluginConfigurationErrors SKIPPED 665: > Task :build-logic:generateExternalPluginSpecBuilders FROM-CACHE ... 855: (see http://t.uber.com/nullaway ) 856: /home/runner/work/jabref/jabref/jablib/src/main/java/org/jabref/logic/externalfiles/LinkedFileHandler.java:177: warning: [NullAway] passing @Nullable parameter 'targetDirectory' where @NonNull is required 857: String uniqueFileName = FileNameUniqueness.generateUniqueFileName(targetDirectory, suggestedFileName); 858: ^ 859: (see http://t.uber.com/nullaway ) 860: /home/runner/work/jabref/jabref/jablib/src/main/java/org/jabref/logic/externalfiles/LinkedFileHandler.java:270: warning: [NullAway] dereferenced expression linkedFile.findIn(databaseContext, filePreferences) 861: .get().getParent().resolve(targetFileName); 862: ^ 863: .get().getParent() is @Nullable 864: (see http://t.uber.com/nullaway ) 865: /home/runner/work/jabref/jabref/jablib/src/main/java/org/jabref/logic/importer/ParserResult.java:51: warning: [NullAway] initializer method does not guarantee @NonNull field file (line 32) is initialized along all control-flow paths (remember to check for exceptions or early returns). 866: public ParserResult(@NonNull BibDatabase database, 867: ^ 868: (see http://t.uber.com/nullaway ) 869: /home/runner/work/jabref/jabref/jablib/src/main/java/org/jabref/logic/importer/ParserResult.java:72: warning: [NullAway] returning @Nullable expression from method with @NonNull return type 870: return errorMessage; 871: ^ ... 1151: > Task :jabgui:processResources 1152: > Task :jabgui:classes 1153: > Task :jabgui:jar 1154: > Task :jablib:generateTestGrammarSource NO-SOURCE 1155: > Task :test-support:compileJava FROM-CACHE 1156: > Task :test-support:processResources NO-SOURCE 1157: > Task :test-support:classes UP-TO-DATE 1158: > Task :test-support:jar 1159: > Task :jablib:compileTestJava FROM-CACHE 1160: > Task :jablib:processTestResources 1161: > Task :jablib:testClasses 1162: > Task :jablib:fetcherTest 1163: OpenJDK 64-Bit Server VM warning: Sharing is only supported for boot loader classes because bootstrap classpath has been appended 1164: > Task :jablib:fetcherTest 1165: �[0K�[1morg.jabref.logic.crawler.CrawlerTest�[m 1166: �[0K�[1m Test �[22mwhetherAllFilesAreCreated()�[31m FAILED�[31m (3m 30s)�[31m 1167: org.opentest4j.AssertionFailedError: expected: <true> but was: <false> 1168: at app//org.jabref.logic.crawler.CrawlerTest.lambda$whetherAllFilesAreCreated$0(CrawlerTest.java:110) 1169: �[m 1170: OpenJDK 64-Bit Server VM warning: Sharing is only supported for boot loader classes because bootstrap classpath has been appended 1171: OpenJDK 64-Bit Server VM warning: Sharing is only supported for boot loader classes because bootstrap classpath has been appended 1172: > Task :jablib:fetcherTest 1173: �[0K�[1morg.jabref.logic.importer.fetcher.ArXivFetcherTest�[m 1174: �[0K�[1m Test �[22mfindFullTextByEprint()�[31m FAILED�[31m 1175: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]> 1176: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByEprint(ArXivFetcherTest.java:207) 1177: �[m 1178: �[0K�[1m Test �[22mfindFullTextByTitleAndPartOfAuthor()�[31m FAILED�[31m 1179: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/cond-mat/0406246v1]> but was: <Optional[https://arxiv.org/pdf/cond-mat/0406246v1]> 1180: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByTitleAndPartOfAuthor(ArXivFetcherTest.java:259) 1181: �[m 1182: �[0K�[1m Test �[22mfindFullTextByTitleWithCurlyBracket()�[31m FAILED�[31m 1183: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/2010.15942v3]> but was: <Optional.empty> 1184: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByTitleWithCurlyBracket(ArXivFetcherTest.java:235) 1185: �[m 1186: �[0K�[1m Test �[22msearchWithHttpsUrlNotTrimmed()�[31m FAILED�[31m 1187: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 1188: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 1205: copyright = {arXiv.org perpetual, non-exclusive license}, 1206: date = {2014-05-09}, 1207: doi = {10.48550/ARXIV.1405.2249}, 1208: eprint = {1405.2249}, 1209: eprintclass = {math-ph}, 1210: eprinttype = {arXiv}, 1211: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 1212: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 1213: publisher = {arXiv}, 1214: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 1215: year = {2014}, 1216: _jabref_shared = {sharedId: -1, version: 1} 1217: }]> 1218: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchWithHttpsUrlNotTrimmed(ArXivFetcherTest.java:395) 1219: �[m 1220: �[0K�[1m Test �[22mfindFullTextByEprintWithPrefix()�[31m FAILED�[31m 1221: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]> 1222: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByEprintWithPrefix(ArXivFetcherTest.java:213) 1223: �[m 1224: �[0K�[1m Test �[22msearchEntryByIdWith4DigitsAndPrefixAndNotTrimmed()�[31m FAILED�[31m 1225: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 1226: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 1243: copyright = {arXiv.org perpetual, non-exclusive license}, 1244: date = {2014-05-09}, 1245: doi = {10.48550/ARXIV.1405.2249}, 1246: eprint = {1405.2249}, 1247: eprintclass = {math-ph}, 1248: eprinttype = {arXiv}, 1249: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 1250: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 1251: publisher = {arXiv}, 1252: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 1253: year = {2014}, 1254: _jabref_shared = {sharedId: -1, version: 1} 1255: }]> 1256: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByIdWith4DigitsAndPrefixAndNotTrimmed(ArXivFetcherTest.java:356) 1257: �[m 1258: �[0K�[1m Test �[22mfindFullTextByEprintWithUnknownDOI()�[31m FAILED�[31m 1259: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/1603.06570v1]> but was: <Optional[https://arxiv.org/pdf/1603.06570v1]> 1260: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByEprintWithUnknownDOI(ArXivFetcherTest.java:221) 1261: �[m 1262: �[0K�[1m Test �[22msupportsPhraseSearch()�[31m FAILED�[31m 1263: org.jabref.logic.importer.FetcherException: arXiv API request failed 1264: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.supportsPhraseSearch(ArXivFetcherTest.java:414) 1265: �[m 1266: �[0K�[1m Test �[22msearchEntryByPartOfTitleWithAcuteAccent()�[31m FAILED�[31m 1267: org.opentest4j.AssertionFailedError: expected: <[@article{https://doi.org/10.48550/arxiv.1405.2249, 1268: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 1270: copyright = {arXiv.org perpetual, non-exclusive license}, 1271: date = {2014-05-09}, 1272: doi = {10.48550/ARXIV.1405.2249}, 1273: eprint = {1405.2249}, 1274: eprintclass = {math-ph}, 1275: eprinttype = {arXiv}, 1276: file = {:http://arxiv.org/pdf/1405.2249v1:PDF}, 1277: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 1278: publisher = {arXiv}, 1279: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 1280: year = {2014}, 1281: _jabref_shared = {sharedId: -1, version: 1} 1282: }]> but was: <[]> 1283: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByPartOfTitleWithAcuteAccent(ArXivFetcherTest.java:308) 1284: �[m 1285: �[0K�[1m Test �[22mfindFullTextByTitleWithColonAndUrlWithoutEprint()�[31m FAILED�[31m 1286: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/2002.10248v4]> but was: <Optional[https://arxiv.org/pdf/2002.10248v4]> 1287: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByTitleWithColonAndUrlWithoutEprint(ArXivFetcherTest.java:251) 1288: �[m 1289: �[0K�[1m Test �[22mretrievePartialResultWhenCannotGetInformationFromUserAssignedDOI()�[31m FAILED�[33m (1s)�[31m 1290: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1701.00587, 1291: abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.}, ... 1310: date = {2017-01-03}, 1311: doi = {10.1073/pnas.1617932114}, 1312: eprint = {1701.00587}, 1313: eprintclass = {q-bio.CB}, 1314: eprinttype = {arXiv}, 1315: file = {:https://arxiv.org/pdf/1701.00587v1:PDF}, 1316: journal = {PNAS December 27, 2016 vol. 113 no. 52 15000-15005}, 1317: keywords = {Cell Behavior (q-bio.CB), FOS: Biological sciences}, 1318: publisher = {arXiv}, 1319: title = {Interrogating the Escherichia coli cell cycle by cell dimension perturbations}, 1320: year = {2017}, 1321: _jabref_shared = {sharedId: -1, version: 1} 1322: }]> 1323: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.retrievePartialResultWhenCannotGetInformationFromUserAssignedDOI(ArXivFetcherTest.java:542) 1324: �[m 1325: �[0K�[1m Test �[22msupportsBooleanANDSearch()�[31m FAILED�[31m 1326: org.opentest4j.AssertionFailedError: expected: <[@article{B_scher_2020, 1327: abstract = {Interfaces in tissues are ubiquitous, both between tissue and environment as well as between populations of different cell types. The propagation of an interface can be driven mechanically. % e.g. by a difference in the respective homeostatic stress of the different cell types. Computer simulations of growing tissues are employed to study the stability of the interface between two tissues on a substrate. From a mechanical perspective, the dynamics and stability of this system is controlled mainly by four parameters of the respective tissues: (i) the homeostatic stress (ii) cell motility (iii) tissue viscosity and (iv) substrate friction. For propagation driven by a difference in homeostatic stress, the interface is stable for tissue-specific substrate friction even for very large differences of homeostatic stress; however, it becomes unstable above a critical stress difference when the tissue with the larger homeostatic stress has a higher viscosity. A small difference in directed bulk motility between the two tissues suffices to result in propagation with a stable interface, even for otherwise identical tissues. Larger differences in motility force, however, result in a finite-wavelength instability of the interface. Interestingly, the instability is apparently bound by nonlinear effects and the amplitude of the interface undulations only grows to a finite value in time.}, ... 1356: file = {:https://arxiv.org/pdf/2003.04601v1:PDF}, 1357: issn = {1367-2630}, 1358: journal = {New J. Phys., 22, 083005 (2020)}, 1359: keywords = {Tissues and Organs (q-bio.TO), FOS: Biological sciences}, 1360: month = {#aug#}, 1361: number = {8}, 1362: pages = {083005}, 1363: publisher = {IOP Publishing}, 1364: title = {Instability and fingering of interfaces in growing tissue}, 1365: volume = {22}, 1366: year = {2020}, 1367: _jabref_shared = {sharedId: -1, version: 1} 1368: }]> 1369: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.supportsBooleanANDSearch(ArXivFetcherTest.java:474) 1370: �[m 1371: �[0K�[1m Test �[22mcanReplicateArXivOnlySearchByPassingNullParameter()�[31m FAILED�[31m 1372: org.opentest4j.AssertionFailedError: expected: <Optional[@article{, 1373: abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.}, ... 1386: abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.}, 1387: author = {Hai Zheng and Po-Yi Ho and Meiling Jiang and Bin Tang and Weirong Liu and Dengjin Li and Xuefeng Yu and Nancy E. Kleckner and Ariel Amir and Chenli Liu}, 1388: date = {2017-01-03}, 1389: doi = {10.1073/pnas.1617932114}, 1390: eprint = {1701.00587}, 1391: eprintclass = {q-bio.CB}, 1392: eprinttype = {arXiv}, 1393: file = {:https://arxiv.org/pdf/1701.00587v1:PDF}, 1394: journal = {PNAS December 27, 2016 vol. 113 no. 52 15000-15005}, 1395: keywords = {q-bio.CB}, 1396: title = {Interrogating the Escherichia coli cell cycle by cell dimension perturbations}, 1397: _jabref_shared = {sharedId: -1, version: 1} 1398: }]> 1399: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.canReplicateArXivOnlySearchByPassingNullParameter(ArXivFetcherTest.java:516) 1400: �[m 1401: �[0K�[1m Test �[22msearchEntryByIdWith4DigitsAndVersion()�[31m FAILED�[31m 1402: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 1403: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 1420: copyright = {arXiv.org perpetual, non-exclusive license}, 1421: date = {2014-05-09}, 1422: doi = {10.48550/ARXIV.1405.2249}, 1423: eprint = {1405.2249}, 1424: eprintclass = {math-ph}, 1425: eprinttype = {arXiv}, 1426: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 1427: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 1428: publisher = {arXiv}, 1429: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 1430: year = {2014}, 1431: _jabref_shared = {sharedId: -1, version: 1} 1432: }]> 1433: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByIdWith4DigitsAndVersion(ArXivFetcherTest.java:341) 1434: �[m 1435: �[0K�[1m Test �[22msupportsPhraseSearchAndMatchesExact()�[31m FAILED�[31m 1436: org.opentest4j.AssertionFailedError: expected: <@article{https://doi.org/10.48550/arxiv.2009.10618, 1437: abstract = {Context: Data Mining (DM) method has been evolving year by year and as of today there is also the enhancement of DM technique that can be run several times faster than the traditional one, called Distributed Data Mining (DDM). It is not a new field in data processing actually, but in the recent years many researchers have been paying more attention on this area. Problems: The number of publication regarding DDM in high reputation journals and conferences has increased significantly. It makes difficult for researchers to gain a comprehensive view of DDM that require further research. Solution: We conducted a systematic literature review to map the previous research in DDM field. Our objective is to provide the motivation for new research by identifying the gap in DDM field as well as the hot area itself. Result: Our analysis came up with some conclusions by answering 7 research questions proposed in this literature review. In addition, the taxonomy of DDM research area is presented in this paper. Finally, this systematic literature review provides the statistic of development of DDM since 2000 to 2015, in which this will help the future researchers to have a comprehensive overview of current situation of DDM.}, ... 1454: copyright = {arXiv.org perpetual, non-exclusive license}, 1455: date = {2020-09-14}, 1456: doi = {10.48550/ARXIV.2009.10618}, 1457: eprint = {2009.10618}, 1458: eprintclass = {cs.DC}, 1459: eprinttype = {arXiv}, 1460: file = {:https://arxiv.org/pdf/2009.10618v1:PDF}, 1461: keywords = {Distributed / Parallel / Cluster Computing (cs.DC), Machine Learning (cs.LG), FOS: Computer and information sciences}, 1462: publisher = {arXiv}, 1463: title = {A Survey and Taxonomy of Distributed Data Mining Research Studies: A Systematic Literature Review}, 1464: year = {2020}, 1465: _jabref_shared = {sharedId: -1, version: 1} 1466: }> 1467: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.supportsPhraseSearchAndMatchesExact(ArXivFetcherTest.java:443) 1468: [/[] 1469: �[0K�[1m Test �[22msearchWithHttpUrl()�[31m FAILED�[31m 1470: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 1471: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 1488: copyright = {arXiv.org perpetual, non-exclusive license}, 1489: date = {2014-05-09}, 1490: doi = {10.48550/ARXIV.1405.2249}, 1491: eprint = {1405.2249}, 1492: eprintclass = {math-ph}, 1493: eprinttype = {arXiv}, 1494: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 1495: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 1496: publisher = {arXiv}, 1497: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 1498: year = {2014}, 1499: _jabref_shared = {sharedId: -1, version: 1} 1500: }]> 1501: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchWithHttpUrl(ArXivFetcherTest.java:385) 1502: �[m 1503: �[0K�[1m Test �[22msearchEntryByPartOfTitle()�[31m FAILED�[31m 1504: org.opentest4j.AssertionFailedError: expected: <[@article{https://doi.org/10.48550/arxiv.1811.10364, 1505: abstract = {Recommender systems in academia are not widely available. This may be in part due to the difficulty and cost of developing and maintaining recommender systems. Many operators of academic products such as digital libraries and reference managers avoid this effort, although a recommender system could provide significant benefits to their users. In this paper, we introduce Mr. DLib's "Recommendations as-a-Service" (RaaS) API that allows operators of academic products to easily integrate a scientific recommender system into their products. Mr. DLib generates recommendations for research articles but in the future, recommendations may include call for papers, grants, etc. Operators of academic products can request recommendations from Mr. DLib and display these recommendations to their users. Mr. DLib can be integrated in just a few hours or days; creating an equivalent recommender system from scratch would require several months for an academic operator. Mr. DLib has been used by GESIS Sowiport and by the reference manager JabRef. Mr. DLib is open source and its goal is to facilitate the application of, and research on, scientific recommender systems. In this paper, we present the motivation for Mr. DLib, the architecture and details about the effectiveness. Mr. DLib has delivered 94m recommendations over a span of two years with an average click-through rate of 0.12%.}, ... 1522: copyright = {arXiv.org perpetual, non-exclusive license}, 1523: date = {2018-11-26}, 1524: doi = {10.48550/ARXIV.1811.10364}, 1525: eprint = {1811.10364}, 1526: eprintclass = {cs.IR}, 1527: eprinttype = {arXiv}, 1528: file = {:https://arxiv.org/pdf/1811.10364v1:PDF}, 1529: keywords = {Information Retrieval (cs.IR), Artificial Intelligence (cs.AI), Digital Libraries (cs.DL), Machine Learning (cs.LG), FOS: Computer and information sciences}, 1530: publisher = {arXiv}, 1531: title = {The Architecture of Mr. DLib's Scientific Recommender-System API}, 1532: year = {2018}, 1533: _jabref_shared = {sharedId: -1, version: 1} 1534: }]> 1535: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByPartOfTitle(ArXivFetcherTest.java:302) 1536: �[m 1537: �[0K�[1m Test �[22mretrievePartialResultWhenCannotGetInformationFromArXivAssignedDOI()�[31m FAILED�[31m 1538: org.opentest4j.AssertionFailedError: expected: <Optional[@article{Zheng_2016, 1539: abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.}, ... 1566: file = {:https://arxiv.org/pdf/1701.00587v1:PDF}, 1567: issn = {1091-6490}, 1568: journal = {PNAS December 27, 2016 vol. 113 no. 52 15000-15005}, 1569: keywords = {q-bio.CB}, 1570: month = {#dec#}, 1571: number = {52}, 1572: pages = {15000--15005}, 1573: publisher = {Proceedings of the National Academy of Sciences}, 1574: title = {Interrogating the Escherichia coli cell cycle by cell dimension perturbations}, 1575: volume = {113}, 1576: year = {2016}, 1577: _jabref_shared = {sharedId: -1, version: 1} 1578: }]> 1579: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.retrievePartialResultWhenCannotGetInformationFromArXivAssignedDOI(ArXivFetcherTest.java:572) 1580: �[m 1581: �[0K�[1m Test �[22msearchEntryByOldId()�[31m FAILED�[31m 1582: org.opentest4j.AssertionFailedError: expected: <Optional[@article{2003, 1583: abstract = {Multi-electron production is studied at high electron transverse momentum in positron- and electron-proton collisions using the H1 detector at HERA. The data correspond to an integrated luminosity of 115 pb-1. Di-electron and tri-electron event yields are measured. Cross sections are derived in a restricted phase space region dominated by photon-photon collisions. In general good agreement is found with the Standard Model predictions. However, for electron pair invariant masses above 100 GeV, three di-electron events and three tri-electron events are observed, compared to Standard Model expectations of 0.30 pm 0.04 and 0.23 pm 0.04, respectively.}, ... 1612: file = {:https://arxiv.org/pdf/hep-ex/0307015v1:PDF}, 1613: issn = {1434-6052}, 1614: journal = {Eur.Phys.J.C31:17-29,2003}, 1615: keywords = {High Energy Physics - Experiment (hep-ex), FOS: Physical sciences}, 1616: month = {#oct#}, 1617: number = {1}, 1618: pages = {17--29}, 1619: publisher = {Springer Science and Business Media LLC}, 1620: title = {Multi-Electron Production at High Transverse Momenta in ep Collisions at HERA}, 1621: volume = {31}, 1622: year = {2003}, 1623: _jabref_shared = {sharedId: -1, version: 1} 1624: }]> 1625: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByOldId(ArXivFetcherTest.java:336) 1626: �[m 1627: �[0K�[1m Test �[22mnoSupportsAuthorSearchWithLastFirstName()�[31m FAILED�[31m (11.1s)�[31m 1628: org.opentest4j.AssertionFailedError: expected: <[]> but was: <[@article{https://doi.org/10.48550/arxiv.hep-ex/0202036, 1629: abstract = {This paper has been withdrawn by the author(s)}, ... 1844: abstract = {Explorables with interactive, multimodal content, openly available on the web, are a promising medium for education. Yet authoring such explorables requires web development expertise, excluding most educators and students from the authoring and remixing process. Some tools are available to reduce this barrier of entry and others are in development, making a method to evaluate these new tools necessary. On the basis of the software quality model ISO 25010, empirical results, and domain modeling, we derive the Explorable Authoring Requirements (EAR) as a requirements catalogue explorable authoring tools should implement. We then outline a future research design to operationalize EAR.}, 1845: archiveprefix = {arXiv}, 1846: author = {Salmen, Frederic and Schroeder, Ulrik}, 1847: copyright = {Creative Commons Attribution Share Alike 4.0 International}, 1848: doi = {10.48550/ARXIV.2403.17714}, 1849: eprint = {2403.17714}, 1850: file = {:https://arxiv.org/pdf/2403.17714v1:PDF}, 1851: keywords = {Human-Computer Interaction (cs.HC), FOS: Computer and information sciences}, 1852: month = {#mar#}, 1853: primaryclass = {cs.HC}, 1854: publisher = {arXiv}, 1855: title = {Evaluating Authoring Tools with the Explorable Authoring Requirements}, 1856: year = {2024}, 1857: _jabref_shared = {sharedId: -1, version: 1} 1858: }, @article{Ghilezan_2016, 1859: abstract = {Security requirements in distributed software systems are inherently dynamic. In the case of authorization policies, resources are meant to be accessed only by authorized parties, but the authorization to access a resource may be dynamically granted/yielded. We describe ongoing work on a model for specifying communication and dynamic authorization handling. We build upon the pi-calculus so as to enrich communication-based systems with authorization specification and delegation; here authorizations regard channel usage and delegation refers to the act of yielding an authorization to another party. Our model includes: (i) a novel scoping construct for authorization, which allows to specify authorization boundaries, and (ii) communication primitives for authorizations, which allow to pass around authorizations to act on a given channel. An authorization error may consist in, e.g., performing an action along a name which is not under an appropriate authorization scope. We introduce a typing discipline that ensures that processes never reduce to authorization errors, even when authorizations are dynamically delegated.}, 1860: archiveprefix = {arXiv}, ... 1963: author = {Yang, Han and Li, Shaofeng and Dong, Tian and Xu, Xiangyu and Liu, Guangchi and Ling, Zhen}, 1964: copyright = {arXiv.org perpetual, non-exclusive license}, 1965: doi = {10.48550/ARXIV.2512.10600}, 1966: eprint = {2512.10600}, 1967: file = {:https://arxiv.org/pdf/2512.10600v1:PDF}, 1968: keywords = {Cryptography and Security (cs.CR), Machine Learning (cs.LG), FOS: Computer and information sciences}, 1969: month = {#dec#}, 1970: primaryclass = {cs.CR}, 1971: publisher = {arXiv}, 1972: title = {Authority Backdoor: A Certifiable Backdoor Mechanism for Authoring DNNs}, 1973: year = {2025}, 1974: _jabref_shared = {sharedId: -1, version: 1} 1975: }]> 1976: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.noSupportsAuthorSearchWithLastFirstName(ArXivFetcherTest.java:183) 1977: �[m 1978: �[0K�[1m Test �[22mfindFullTextByTitle()�[31m FAILED�[31m 1979: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/cond-mat/0406246v1]> but was: <Optional[https://arxiv.org/pdf/cond-mat/0406246v1]> 1980: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByTitle(ArXivFetcherTest.java:228) 1981: �[m 1982: �[0K�[1m Test �[22msearchEntryByIdWith4DigitsAndPrefix()�[31m FAILED�[31m 1983: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 1984: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 2001: copyright = {arXiv.org perpetual, non-exclusive license}, 2002: date = {2014-05-09}, 2003: doi = {10.48550/ARXIV.1405.2249}, 2004: eprint = {1405.2249}, 2005: eprintclass = {math-ph}, 2006: eprinttype = {arXiv}, 2007: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 2008: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 2009: publisher = {arXiv}, 2010: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 2011: year = {2014}, 2012: _jabref_shared = {sharedId: -1, version: 1} 2013: }]> 2014: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByIdWith4DigitsAndPrefix(ArXivFetcherTest.java:351) 2015: �[m 2016: �[0K�[1m Test �[22mfindFullTextByDOI()�[31m FAILED�[31m 2017: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/cond-mat/0406246v1]> but was: <Optional[https://arxiv.org/pdf/cond-mat/0406246v1]> 2018: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByDOI(ArXivFetcherTest.java:201) 2019: �[m 2020: �[0K�[1m Test �[22mfindFullTextByTitleWithColonAndJournalWithoutEprint()�[31m FAILED�[31m 2021: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/2002.10248v4]> but was: <Optional[https://arxiv.org/pdf/2002.10248v4]> 2022: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByTitleWithColonAndJournalWithoutEprint(ArXivFetcherTest.java:243) 2023: �[m 2024: �[0K�[1m Test �[22mretrievePureArxivEntryWhenAllDOIFetchingFails()�[31m FAILED�[31m 2025: org.opentest4j.AssertionFailedError: expected: <Optional[@article{, 2026: abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.}, ... 2039: abstract = {Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.}, 2040: author = {Hai Zheng and Po-Yi Ho and Meiling Jiang and Bin Tang and Weirong Liu and Dengjin Li and Xuefeng Yu and Nancy E. Kleckner and Ariel Amir and Chenli Liu}, 2041: date = {2017-01-03}, 2042: doi = {10.1073/pnas.1617932114}, 2043: eprint = {1701.00587}, 2044: eprintclass = {q-bio.CB}, 2045: eprinttype = {arXiv}, 2046: file = {:https://arxiv.org/pdf/1701.00587v1:PDF}, 2047: journal = {PNAS December 27, 2016 vol. 113 no. 52 15000-15005}, 2048: keywords = {q-bio.CB}, 2049: title = {Interrogating the Escherichia coli cell cycle by cell dimension perturbations}, 2050: _jabref_shared = {sharedId: -1, version: 1} 2051: }]> 2052: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.retrievePureArxivEntryWhenAllDOIFetchingFails(ArXivFetcherTest.java:497) 2053: �[m 2054: �[0K�[1m Test �[22msearchEntryByIdWith4Digits()�[31m FAILED�[31m 2055: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 2056: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 2073: copyright = {arXiv.org perpetual, non-exclusive license}, 2074: date = {2014-05-09}, 2075: doi = {10.48550/ARXIV.1405.2249}, 2076: eprint = {1405.2249}, 2077: eprintclass = {math-ph}, 2078: eprinttype = {arXiv}, 2079: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 2080: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 2081: publisher = {arXiv}, 2082: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 2083: year = {2014}, 2084: _jabref_shared = {sharedId: -1, version: 1} 2085: }]> 2086: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchEntryByIdWith4Digits(ArXivFetcherTest.java:346) 2087: �[m 2088: �[0K�[1m Test �[22mfindFullTextByTitleWithCurlyBracketAndPartOfAuthor()�[31m FAILED�[31m 2089: org.opentest4j.AssertionFailedError: expected: <Optional[http://arxiv.org/pdf/2010.15942v3]> but was: <Optional[https://arxiv.org/pdf/2010.15942v3]> 2090: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.findFullTextByTitleWithCurlyBracketAndPartOfAuthor(ArXivFetcherTest.java:267) 2091: �[m 2092: �[0K�[1m Test �[22msearchWithHttpsUrl()�[31m FAILED�[31m 2093: org.opentest4j.AssertionFailedError: expected: <Optional[@article{https://doi.org/10.48550/arxiv.1405.2249, 2094: abstract = {A general slice theorem for the action of a Fr'echet Lie group on a Fr'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.}, ... 2113: doi = {10.48550/ARXIV.1405.2249}, 2114: eprint = {1405.2249}, 2115: eprintclass = {math-ph}, 2116: eprinttype = {arXiv}, 2117: file = {:https://arxiv.org/pdf/1405.2249v1:PDF}, 2118: keywords = {Mathematical Physics (math-ph), Differential Geometry (math.DG), Symplectic Geometry (math.SG), FOS: Physical sciences, FOS: Mathematics, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42}, 2119: publisher = {arXiv}, 2120: title = {Slice theorem for Fréchet group actions and covariant symplectic field theory}, 2121: year = {2014}, 2122: _jabref_shared = {sharedId: -1, version: 1} 2123: }]> 2124: at app//org.jabref.logic.importer.fetcher.ArXivFetcherTest.searchWithHttpsUrl(ArXivFetcherTest.java:390) 2125: �[m 2126: �[0K�[1morg.jabref.logic.importer.fetcher.CompositeIdFetcherTest�[m 2127: �[0K�[1m performSearchByIdReturnsCorrectEntryForIdentifier(String, BibEntry, String)�[m 2128: �[0K�[1m Test �[22m1 "performSearchByIdReturnsCorrectEntryForArXivId"�[31m FAILED�[33m (1s)�[31m 2129: org.opentest4j.AssertionFailedError: expected: <Optional[@article{Cunningham_2022, 2130: abstract = {In the era of large-scale spectroscopic surveys in the Local Group (LG), we can explore using chemical abundances of halo stars to study the star formation and chemical enrichment histories of the dwarf galaxy progenitors of the Milky Way (MW) and M31 stellar halos. In this paper, we investigate using the Chemical Abundance Ratio Distributions (CARDs) of seven stellar halos from the Latte suite of FIRE-2 simulations. We attempt to infer galaxies' assembly histories by modelling the CARDs of the stellar halos of the Latte galaxies as a linear combination of template CARDs from disrupted dwarfs, with different stellar masses $M_{star}$ and quenching times $t_{100}$. We present a method for constructing these templates using present-day dwarf galaxies. For four of the seven Latte halos studied in this work, we recover the mass spectrum of accreted dwarfs to a precision of $<10%$. For the fraction of mass accreted as a function of $t_{100}$, we find residuals of $20-30%$ for five of the seven simulations. We discuss the failure modes of this method, which arise from the diversity of star formation and chemical enrichment histories dwarf galaxies can take. These failure cases can be robustly identified by the high model residuals. Though the CARDs modeling method does not successfully infer the assembly histories in these cases, the CARDs of these disrupted dwarfs contain signatures of their unusual formation histories. Our results are promising for using CARDs to learn more about the histories of the progenitors of the MW and M31 stellar halos.}, 2131: author = {Cunningham, Emily C. and Sanderson, Robyn E. and Johnston, Kathryn V. and Panithanpaisal, Nondh and Ness, Melissa K. and Wetzel, Andrew and Loebman, Sarah R. and Escala, Ivanna and Horta, Danny and Faucher-Giguère, Claude-André}, ... 2136: eprintclass = {astro-ph.GA}, 2137: eprinttype = {arXiv}, 2138: file = {:http://arxiv.org/pdf/2110.02957v1:PDF}, 2139: issn = {1538-4357}, 2140: journal = {The Astrophysical Journal}, 2141: keywords = {Astrophysics of Galaxies (astro-ph.GA), FOS: Physical sciences}, 2142: month = {#aug#}, 2143: number = {2}, 2144: pages = {172}, 2145: publisher = {American Astronomical Society}, 2146: title = {Reading the CARDs: the Imprint of Accretion History in the Chemical Abundances of the Milky Way's Stellar Halo}, 2147: volume = {934}, 2148: year = {2021}, 2149: _jabref_shared = {sharedId: -1, version: 1} 2150: }]> but was: <Optional[@article{Cunningham_2022, 2151: abstract = {In the era of large-scale spectroscopic surveys in the Local Group (LG), we can explore using chemical abundances of halo stars to study the star formation and chemical enrichment histories of the dwarf galaxy progenitors of the Milky Way (MW) and M31 stellar halos. In this paper, we investigate using the Chemical Abundance Ratio Distributions (CARDs) of seven stellar halos from the Latte suite of FIRE-2 simulations. We attempt to infer galaxies' assembly histories by modelling the CARDs of the stellar halos of the Latte galaxies as a linear combination of template CARDs from disrupted dwarfs, with different stellar masses $M_{star}$ and quenching times $t_{100}$. We present a method for constructing these templates using present-day dwarf galaxies. For four of the seven Latte halos studied in this work, we recover the mass spectrum of accreted dwarfs to a precision of $<10%$. For the fraction of mass accreted as a function of $t_{100}$, we find residuals of $20-30%$ for five of the seven simulations. We discuss the failure modes of this method, which arise from the diversity of star formation and chemical enrichment histories dwarf galaxies can take. These failure cases can be robustly identified by the high model residuals. Though the CARDs modeling method does not successfully infer the assembly histories in these cases, the CARDs of these disrupted dwarfs contain signatures of their unusual formation histories. Our results are promising for using CARDs to learn more about the histories of the progenitors of the MW and M31 stellar halos.}, 2152: author = {Cunningham, Emily C. and Sanderson, Robyn E. and Johnston, Kathryn V. and Panithanpaisal, Nondh and Ness, Melissa K. and Wetzel, Andrew and Loebman, Sarah R. and Escala, Ivanna and Horta, Danny and Faucher-Giguère, Claude-André}, ... 2160: issn = {1538-4357}, 2161: journal = {The Astrophysical Journal}, 2162: keywords = {Astrophysics of Galaxies (astro-ph.GA), FOS: Physical sciences}, 2163: month = {#aug#}, 2164: number = {2}, 2165: pages = {172}, 2166: publisher = {American Astronomical Society}, 2167: title = {Reading the CARDs: the Imprint of Accretion History in the Chemical Abundances of the Milky Way's Stellar Halo}, 2168: volume = {934}, 2169: year = {2021}, 2170: _jabref_shared = {sharedId: -1, version: 1} 2171: }]> 2172: at app//org.jabref.logic.importer.fetcher.CompositeIdFetcherTest.performSearchByIdReturnsCorrectEntryForIdentifier(CompositeIdFetcherTest.java:134) 2173: �[m 2174: �[0K�[1morg.jabref.logic.importer.fetcher.CrossRefTest�[m 2175: �[0K�[1m Test �[22mperformSearchByIdFindsPaperWithoutTitle()�[31m FAILED�[31m 2176: org.opentest4j.AssertionFailedError: expected: <Optional[@article{, 2177: author = {Leo Breiman}, ... 2188: author = {Leo Breiman}, 2189: doi = {10.1023/a:1010933404324}, 2190: issn = {0885-6125}, 2191: journal = {Machine Learning}, 2192: number = {1}, 2193: pages = {5-32}, 2194: publisher = {Springer Science and Business Media LLC}, 2195: title = {Random Forests}, 2196: volume = {45}, 2197: year = {2001}, 2198: _jabref_shared = {sharedId: -1, version: 1} 2199: }]> 2200: at app//org.jabref.logic.importer.fetcher.CrossRefTest.performSearchByIdFindsPaperWithoutTitle(CrossRefTest.java:136) 2201: �[m 2202: �[0K�[1morg.jabref.logic.importer.fetcher.ISIDOREFetcherTest�[m 2203: �[0K�[1m Test �[22mauthor()�[31m FAILED�[31m 2204: org.jabref.logic.importer.FetcherException: Error getting response code 2205: at app//org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.author(ISIDOREFetcherTest.java:103) 2206: Caused by: javax.net.ssl.SSLHandshakeException: (certificate_unknown) PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2207: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.author(ISIDOREFetcherTest.java:103) 2208: Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2209: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.author(ISIDOREFetcherTest.java:103) 2210: Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2211: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.author(ISIDOREFetcherTest.java:103) 2212: �[m 2213: �[0K�[1m Test �[22mcheckThesis()�[31m FAILED�[31m 2214: org.jabref.logic.importer.FetcherException: Error getting response code 2215: at app//org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.checkThesis(ISIDOREFetcherTest.java:69) 2216: Caused by: javax.net.ssl.SSLHandshakeException: (certificate_unknown) PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2217: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.checkThesis(ISIDOREFetcherTest.java:69) 2218: Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2219: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.checkThesis(ISIDOREFetcherTest.java:69) 2220: Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2221: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.checkThesis(ISIDOREFetcherTest.java:69) 2222: �[m 2223: �[0K�[1m Test �[22mnoResults()�[31m FAILED�[31m 2224: org.jabref.logic.importer.FetcherException: Error getting response code 2225: at app//org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.noResults(ISIDOREFetcherTest.java:97) 2226: Caused by: javax.net.ssl.SSLHandshakeException: (certificate_unknown) PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2227: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.noResults(ISIDOREFetcherTest.java:97) 2228: Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2229: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.noResults(ISIDOREFetcherTest.java:97) 2230: Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target 2231: at org.jabref.logic.importer.fetcher.ISIDOREFetcherTest.noResults(ISIDOREFetcherTest.java:97) 2232: �[m 2233: �[0K�[1morg.jabref.logic.importer.fetcher.LibraryOfCongressTest�[m 2234: �[0K�[1m Test �[22mperformSearchById()�[31m FAILED�[31m (30s)�[31m 2235: org.jabref.logic.importer.FetcherException: Error getting response code 2236: at app//org.jabref.logic.importer.fetcher.LibraryOfCongressTest.performSearchById(LibraryOfCongressTest.java:53) 2237: Caused by: java.net.SocketTimeoutException: Connect timed out 2238: at org.jabref.logic.importer.fetcher.LibraryOfCongressTest.performSearchById(LibraryOfCongressTest.java:53) 2239: �[m 2240: �[0K�[1m Test �[22mperformSearchByInvalidId()�[31m FAILED�[31m (30s)�[31m 2241: org.opentest4j.AssertionFailedError: Unexpected exception type thrown, expected: <org.jabref.logic.importer.FetcherClientException> but was: <org.jabref.logic.importer.FetcherException> ...

Siedlerchr · 2026-02-03T20:36:39Z

      - name: Run OpenRewrite
        run: |
-          ./gradlew --no-configuration-cache :rewriteDryRun
+          ./gradlew --no-configuration-cache :rewriteRun


I thought we want to have dryRun

Look at the later steps. --> name: Output diff

DryRun does not change files. No changed files, no diff

How to output something then?

TBH, IDK why we changed to Dry. Now, it works. Wondered why no complaints were there... It was because, "Dry" - checking, and not complaining even if changes would be required.

* upstream/main: New Crowdin updates (#15035) Use patched Gradle version (#15034) Add OpenAlex-based Citation Fetcher (#15023) Update null annotaitons at EntryBasedFetcher (#15024) Fix CHANGELOG.md test Use _ for unused variables (#15028) Use ubuntu-latest for checkstyle and javadoc Update Gradle Wrapper from 9.3.0-jabref-2 to 9.3.1 (#15021) Use "ubuntu-slim" for most workflows (#15019) Refine GroupsTree (#15013)

…4902 * upstream/main: (23 commits) Some more recipes from OpenRewrite (JabRef#15030) feat: Add PDF Upload endpoint to EntryResource (JabRef#14963) Heuristics also used at batch (JabRef#15025) Fix cleanup-pr.yml New Crowdin updates (JabRef#15035) Use patched Gradle version (JabRef#15034) Add OpenAlex-based Citation Fetcher (JabRef#15023) Update null annotaitons at EntryBasedFetcher (JabRef#15024) Fix CHANGELOG.md test Use _ for unused variables (JabRef#15028) Use ubuntu-latest for checkstyle and javadoc Update Gradle Wrapper from 9.3.0-jabref-2 to 9.3.1 (JabRef#15021) Use "ubuntu-slim" for most workflows (JabRef#15019) Refine GroupsTree (JabRef#15013) New Crowdin updates (JabRef#15018) Added Clear group option (JabRef#15017) Chore(deps): Bump com.uber.nullaway:nullaway from 0.12.15 to 0.13.1 in /versions (JabRef#15006) Chore(deps): Bump tools.jackson:jackson-bom in /versions (JabRef#15007) No rush in Docker building Yaml issue workaround ...

Use "ubuntu-slim" for most actions

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koppor added the dev: ci-cd label Feb 3, 2026

qodo-free-for-open-source-projects Bot added the Review effort 2/5 label Feb 3, 2026

koppor added 7 commits February 3, 2026 19:47

Use ubuntu-latest

ab851e2

Install jq (and update to ubuntu-latest)

3bb551f

Fix link check

81b844b

Fix gradle wrapper

965ed31

Fix gradle wrapper update

6abf398

More triggers

be97c22

Fix on PR run

54852d7

koppor changed the title ~~Use "ubuntu-slim" for most actions~~ Use "ubuntu-slim" for most workflows Feb 3, 2026

koppor and others added 6 commits February 3, 2026 20:40

Fix upload-release

be9be50

Fix OpenRewrite

099a843

Fix issues using OpenRewrite

56084e7

Merge branch 'main' into use-slim

abf88fd

Fix OpenRewrite test

9023c53

Fix indent

68b736e

koppor merged commit 208cf48 into main Feb 3, 2026
56 of 57 checks passed

koppor deleted the use-slim branch February 3, 2026 20:30

Siedlerchr reviewed Feb 3, 2026

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Use "ubuntu-slim" for most workflows#15019

Use "ubuntu-slim" for most workflows#15019
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